Joomla Complicated URL Rewrites

Joomla Complicated URL Rewrites

We are currently creating a new website for the purpose of including a
shopping cart. The problem we have is that we currently rank well for all
of our keywords on google and need to recreate our urls exactly as they
are on our existing Joomla installation.
We have a business that is heavily reliant on our search traffic from
google (we know this is not ideal!). The shopping cart we want to use is
mijoshop (based on opencart)
Our current URL format is
http://www.yahire.com/index.php/chair-hire/folding-chair-hire.html
The default url's for this shopping cart are awful and we can change these
using an SEF plugin but this removes the index.php from all url's so they
would be for example
http://www.yahire.com/chair-hire/folding-chair-hire
We planed to phase out the index.php gradually from the url starting with
index.php/event-accessories then moving on to index.php/chair-hire so that
if one section of our site drops in rank we still have traffic coming in
from the other sections.
Does anybody know of a way to keep some pages containing the index.php/
and some without?
Thanks in advance for any help with this.